An alignment system includes an alignment detector for detecting a relative deviation of the mask and the wafer from a predetermined positional relationship, a stage mechanism for moving the mask relative to the wafer, an interferometer device for producing information related to the movement by the stage mechanism, and a controller for determining an input to be applied to the stage mechanism so as to bring the mask and the wafer into the predetermined positional relationship, on the basis of a detected value obtained through the alignment detector and a measured value obtained through the interferometer device, both being uptaken at the same timing, and for controlling the stage mechanism on the basis of the thus determined input.